Abstract: The present disclosure enables collections of variable heavy chain and variable light chain pairs comprising, in part, germline protein sequences that are pre-selected for functional properties relevant to developability, wherein the collections may be used to select against any antigen using, for example, phage display.

Abstract: A method of providing a prognosis of breast cancer is conducted by analyzing the expression of a group of genes. Gene expression profiles in a variety of medium such as microarrays are included as are kits that contain them.

Abstract: A method of recognizing the development of an Acute Myocardial Infarction (AMI) process in an individual, wherein the method comprises steps of: profiling specific antibody reactivities or biomarkers associated with AMI susceptibility, the profiling comprises steps of: attaching a set of defined antigens to a substrate; obtaining a biological fluid derived specimen from an individual, the specimen containing a specific antibody repertoire; and binding said antibodies of the biological fluid specimen to the attached antigens thereby forming bound antibody antigen complexes; and analyzing results obtained, wherein the presence of the complexes is indicative of AMI.

Abstract: The present invention provides methods and compositions for tagging nucleic acid sequence fragments, e.g., a set of nucleic acid sequence fragments from a single genome, with one or more unique members of a collection of oligonucleotide tags, or sequence tokens, which, in turn, can be identified using a variety of readout platforms. As a general rule, a given sequence token is used once and only once in any tag sequence. In addition, the present invention also provides methods for using the sequence tokens to efficiently determine variations in nucleotide sequences in the associated nucleic acid sequence fragments.

Abstract: Novel polypeptides having the scaffold structure of a C-type lectin-like domain (CTLD) and a randomized loop region for specifically binding a variety of target compounds and also provides nucleic acids encoding the polypeptides. Combinatorial CTLD libraries, methods for constructing the libraries, and methods for screening the libraries to identify and isolate the novel CTLD polypeptides. Libraries of nucleic acids encoding polypeptides having a scaffold CTLD with a randomized loop region, as well as nucleic acid sequences, vectors, and methods for preparing and expressing the libraries. Exemplary nucleic acids useful in the combinatorial libraries are derived from tetranectin and other proteins having a CTLD.

Abstract: The present invention is based in part on the identification of a signature marker profile of immune variables to diagnose an immune mediated disease or for prediction of response to an immune mediated disease therapeutic agent. Additionally, the present invention provides methods for the prediction of response to an immune mediated disease therapeutic agent.

Abstract: A method of detecting circulating melanoma or carcinoma cells in a subject. The method comprises obtaining a body fluid from a subject and detecting the expression of a panel of genes in the body fluid, wherein the expression of the panel of genes indicates the presence of circulating melanoma or carcinoma cells in the subject. Genes useful for detecting melanoma cells includes GalNAc-T, MAGE-A3, MART-1, PAX-3, and TRP-2; genes useful for detecting carcinoma cells include C-Met, MAGE-A3, Stanniocalcin-1, Stanniocalcin-2, mammaglobin, HSP27, GalNAc-T, CK20, and ?-HCG. Also disclosed are kits containing agents for detecting the expression of these genes.

Abstract: The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as “tiers” of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g.

Abstract: The invention provides a microarray and methods for producing a protein microarray. The array comprises multiple nucleic acid molecules immobilized on a substrate, each comprising (i) a protein-binding domain and (ii) a nucleic acid sequence encoding a fusion protein comprising a polypeptide of interest and a DNA-binding protein that binds the protein-binding domain, and one or more fusion proteins produced from the multiple nucleic acid molecules. Each fusion protein is immobilized on the substrate via binding to a nucleic acid sequence comprising the protein-binding domain present on the nucleic acid molecule from which the fusion protein is produced or on the substrate. The invention also provides a method of analyzing protein interactions with, for example, other proteins, lipids and drugs.

Abstract: The present disclosure enables methods of identifying the VH and VL class pairs in the human immune repertoire, determining the VH and VL class pairs that are most prevalent and those having favorable biophysical properties. More specifically, the collections of the present disclosure comprise the most prevalent and/or preferred VH and VL class pairings with highly diversified CDRs.

Abstract: The present invention relates to a method for in vivo molecular evolution of antibody function. According to the present invention, a nucleic acid encoding a CDR that is normally contained in a framework (the “original framework”), which differs from a selected master framework, is amplified from an immunoglobulin gene and is inserted into a nucleic acid encoding the selected master framework. The invention further provides an antibody library, such as a phage display library, and methods of making the same.

Abstract: Methods for determining the susceptibility of a hepatitis C virus (HCV) in a patient to anti-viral agents, particularly cyclophilin inhibitors such as cyclosporine A, are disclosed. The methods include determining the amino acid sequence within a region of the HCV NS5A protein and comparing the viral amino acid sequence to that of a reference strain, wherein the existence of at least one variant/mutation in the viral genome is indicative that the virus is more or less susceptible to anti-viral agents. Also disclosed are isolated polynucleotide molecules, replicons, and kits that can be used to assay the susceptibility of hepatitis HCV in a patient to anti-viral agents.

Abstract: A gene set, kit and method predict the efficiency of anthracyclines-based treatment of breast cancer.

Abstract: A gel microdrop composition is provided. In certain embodiments, the gel microdrop composition contains a polymer matrix, an effector particle that releases an effector molecule into the polymer matrix, a first reporter particle that emits a first optically detectable signal and a second reporter particle that emits a second optically detectable signal that is distinguishable from the first optically detectable signal, where the effector particle and said first and second reporter particles are encapsulated by the polymer matrix. Methods of screening that employ the gel microdrop composition and methods of making the gel microdrop composition are also disclosed.

Abstract: Methods for making a combinatorial antibody library from human germline segments are provided. Also provided are libraries of nucleic acid molecules compiled from germline segments encoding VL chains and libraries of nucleic acid molecules encoding VH chains, and resulting antibody libraries. The libraries are provided as addressable libraries. Methods for screening antibody libraries against a target protein antigen, and the identified or selected antibodies are provided.

Abstract: The present invention relates to eukaryotic host cells having modified oligosaccharides which may be modified further by heterologous expression of a set of glycosyltransferases, sugar transporters and mannosidases to become host-strains for the production of mammalian, e.g., human therapeutic glycoproteins. The invention provides nucleic acid molecules and combinatorial libraries which can be used to successfully target and express mammalian enzymatic activities such as those involved in glycosylation to intracellular compartments in a eukaryotic host cell. The process provides an engineered host cell which can be used to express and target any desirable gene(s) involved in glycosylation. Host cells with modified oligosaccharides are created or selected. N-glycans made in the engineered host cells have a Man5GlcNAc2 core structure which may then be modified further by heterologous expression of one or more enzymes, e.g.

Abstract: The invention provides methods of developing tissue-specific biomarkers of aging, sets of robust biomarkers identified by those methods, and uses of the biomarkers to identify nutrients and other functional ingredients or agents having anti-aging properties.

Abstract: This invention provides modified nucleotide sequences encoding luciferase that have greater expression than wild type luciferase.

Abstract: Focused libraries of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of antibody peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the focused diversity of the family. The libraries have length and sequence diversities that mimic that found in native human antibodies.

Abstract: The invention provides compositions and methods for determining the likelihood of successful treatment with an effective amount of an anti-VEGF antibody or equivalent thereof, in combination with anti-EGFR antibody or equivalent thereof, and, in some aspects in combination with a topoisomerase inhibitor. The methods comprise determining the identity of a gene of interest in a patient sample and correlating the patient's genotype with the predictive response. Patients identified as responsive are then treated with the appropriate therapy.

Abstract: Vectors and methods for the production of influenza viruses suitable as recombinant influenza vaccines in cell culture are provided. Bi-directional expression vectors for use in a multi-plasmid influenza virus expression system are provided.

Abstract: The present invention provides compositions, including vectors, and methods for the rapid subcloning of nucleic acid sequences in vivo and in vitro. In particular, the invention provides vectors used to contain a gene of interest that comprise a sequence-specific recombinase target site. These vectors are used to rapidly transfer the gene or genes of interest into any vector that contains a sequence-specific recombinase target site located downstream of a regulatory element so that the gene of interest may be regulated.

Abstract: A method for determining a prognosis for survival for a patient with breast cancer is described. Also described is method for monitoring the effectiveness of a course of treatment for a patient with breast cancer, and the use of such a method in a kit. A kit determining the level of RINF is also described.

Abstract: MicroRNA (miRNA) profiling of cells showed unique miRNA signatures for each of three Akt isoforms. Among differentially regulated miRNA species, the miR-200 family was downregulated in Akt2-expressing cells. Akt1 knockdown inhibited expression of miR-200 and promoted TGF?-induced epithelial-mesenchymal-transition (EMT) and a stem cell like phenotype. Carcinomas developing in MMTV-cErb2/Akt1?/? mice exhibited increased invasiveness because of EMT induced by miR-200 downregulation. EMT was found to be controlled by miRNA species that are regulated by the balance between Akt1 and Akt2, rather than overall Akt levels.

Abstract: To provide a gene useful for imparting oxygen resistance to a microorganism and use of the gene. The oxygen-resistance-imparting gene encoding a protein selected from among the following proteins (a) to (c): (a) a protein having the amino acid sequence of SEQ ID NO: 2 or 6; (b) a protein which has an amino acid sequence equivalent to the amino acid sequence of (a), except that one to several amino acid residues are deleted, substituted, or added, and which exhibits oxygen-resistance-imparting activity; and (c) a protein which has an amino acid sequence having an identity of 85% or higher to the amino acid sequence of (a), and which exhibits oxygen-resistance-imparting activity.

Abstract: The present invention relates to a method for generating an RNA library or a (poly)peptide library comprising the steps of: (a) providing one or more nucleic acid molecules each comprising i) two or more coding elements (A) each giving rise to an RNA molecule upon transcription and/or a (poly)peptide upon transcription and translation; and ii) linking elements (B) arranged according to the general formula of B(AB)2+n, wherein said linking elements comprise one or more sequence motifs not found in said two or more coding elements allowing specific disruption of the linking elements (B); (b) cloning the nucleic acid molecule of step (a) into a vector; (c) transforming a host cell with the vector obtained in step (b) and propagating said transformed cell; (d) preparing vector DNA from the transformed and propagated cells of step (c); (e) (i) disrupting the vector DNA obtained in step (d) with one or more agents recognizing said one or more sequence motifs of the linking elements or (ii) performing an amplificati

Abstract: The present invention relates to immunoglobulin new antigen receptors (IgNARs) from fish and uses thereof. In particular, the present invention relates to modified IgNAR variable domains and to domains from members of the immunoglobulin superfamily that have been modified to include structural features derived from IgNAR variable domains.

Abstract: A method for assaying a biological sample includes forming sensitized microcapsules filled with unique oligomarkers, capturing sensitized microcapsules in the presence of analytes, releasing oligomarkers from microcapsules and detecting and measuring oligomarkers to detect and quantify presence of analyte in biological sample. Using encapsulated oligomarkers provides for an amplified high sensitivity assay and using plurality of oligomarker types provides for a multiplexed assay.

Abstract: A method of obtaining cut-off expression values should be selected so as to maximise the separation of the respective survival curves of the two groups of patients. Pairs of genes are statistically significant genes are generated by generating a plurality of models, each of which represents a way of partitioning a set of subjects based on the optimal cut-off expression values of the pair of genes. Those gene pairs are identified for which one of the models has a high prognostic significance. Novel survival significant gene sets forming functional modules which could be used to develop specific prognostic and predictive tests are derived.

Abstract: The discovery and validation of a candidate biomarker signature for the diagnosis of sepsis, and more particularly septicemic meliodiosis, based on genomic transcriptional profiling using microarrays is described herein. The microarray technology of the instant invention generates genome-wide transcriptional profiles (>48,000 transcripts) from the whole blood of patients with septicemic melioidosis (n=32), patients with sepsis caused by other pathogens (n=31), and uninfected controls (n=29). Unsupervised analyses demonstrated the existence of a whole blood transcriptional signature distinguishing patients with sepsis from control subjects.

Abstract: This invention describes soluble, monovalent, non-natural protein molecules that can activate NK cells and certain T-cells to attack specific cellular target cells by attaching the NKG2D-binding portions of monovalent MICA or MICB protein, i.e. their ?1-?2 platform domain, to the intended target cell specifically. The ?1-?2 domain is contiguous with a heterologous ?3 domain that has been genetically modified to bind directly or indirectly to the extracellular aspect of the target cell, thereby serving as the targeting domain. The genetic modification to create a non-natural and non-terminal targeting motif within the ?3 domain can include a portion of an antibody, another protein molecule or portion thereof, a peptide, or a non-natural, modified ?3 domain of a MIC protein.

Abstract: Synergistic combinations of gemcitabine with P276-00 or P1446A and their use in the treatment of cancer are disclosed. The invention further describes novel and unique gene signatures comprising gene markers used to monitor the drug response in a subject treated with the said combinations.

Abstract: A gene or protein set includes at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, and possibly 40, 45, 50, 55, 60, 65 genes or proteins, antibodies or hypervariable portion thereof directed against the proteins encoded by these genes.

Abstract: A micro-fluidic device and a method of use are disclosed. The device includes a micro-channel with an inlet port at a first end and an outlet port at a second end. A first fluid, such as air or liquid or both, is disposed in the micro-channel. A focusing structure extends into the micro-channel, whereby when a pulse of a second fluid is introduced to the channel, the pulse advances adjacent sides of the micro-channel at a faster rate than would occur without the focusing structure.

Abstract: The inventors have found a group of genes whose expression in small bronchoscopic tumor samples gives significant predictions of survival. 10 of the 13 genes are indicators of risk, while the other 3 are indicators of survival.

Abstract: The compositions and methods described are directed to gene chips having a plurality of different oligonucleotides with specificity for genes associated with autism spectrum disorders. The invention further provides methods of identifying gene profiles for neurological and psychiatric conditions including autism spectrum disorders, methods of treating such conditions, and methods of identifying therapeutics for the treatment of such neurological and psychiatric conditions.

Abstract: Genes that are deregulated in cancer stem cells (e.g., melanoma stem cells) are disclosed. Methods which involve modulating (e.g., inducing, inhibiting, etc.) the activity of the cancer stem cell associated genes are used to treat individuals having melanoma. Cell surface genes that are upregulated in melanoma stem cells are targeted for the selective isolation, detection, and killing of cancer stem cells in melanoma.

Abstract: The present invention relates to methods of detecting, monitoring and treating prostate cancer (PRC) OR prostatic intraepithelial neoplasia (PIN) or a predisposition to same. Provided for use in the methods is a novel cancer marker, PSPU43, as well as bioassays and kits.

Abstract: A sample is diagnosed with a genechip array by the present disclosure. The sample is automatically diagnosed by devices revealed in the present disclosure for a fast diagnosis having high accuracy.

Abstract: The present invention relates to novel marker sequences for inflammatory prostate diseases, prostate carcinoma and the diagnostic use thereof together with a method for screening of potential active substances for inflammatory prostate diseases, prostate carcinoma by means of these marker sequences. Furthermore, the invention relates to a diagnostic device containing such marker sequences for inflammatory prostate diseases, prostate carcinoma, in particular a protein biochip and the use thereof.

Abstract: A protein scaffold based on a consensus sequence of fibronectin type III (FN3) proteins, such as the tenth FN3 repeat from human fibronectin (human Tenascin), including isolated nucleic acids that encode a protein scaffold, vectors, host cells, and methods of making and using thereof, exhibit enhanced thermal and chemical stability while presenting six modifiable loop domains which can be engineered to form a binding partner capable of binding to a target for applications in diagnostic and/or therapeutic compositions, methods and devices.

Abstract: The present invention relates to a DNA chip showing specific responses to a human intestinal normal bacterial flora and a method for estimating harmness to the human bodies due to the change of the human intestinal normal bacterial flora using the DNA chip.

Abstract: A glycosyl transferase from Chinese hamster and related methods are described.

Abstract: The present invention relates to a specific set of genes useful for determining the efficacy of a treatment against multiple sclerosis (MS). Further, the invention provides an array of these genes useful for evaluating efficacy of a MS treatment. Also provided are methods for evaluating efficacy of an MS treatment and a method for detecting neutralizing antibodies in patient response to interferon?-1B treatment of MS.

Abstract: The present invention provides methods of detecting cancer using biomarkers.

Abstract: Gene panels, biomarker panels and microarrays relating to lipid formation in stratum corneum of human skin as a function of extrinsic and/or intrinsic aging conditions, and methods for assessing the age status of human skin, methods for identifying or evaluating an agent as effective for improving stratum corneum barrier maintenance and/or repair properties in aged skin, and cosmetic composition comprising the identified agents are all provided.

Abstract: It is disclosed herein that members of the protein tyrosine kinase (PTK) family are highly mutated in patients with melanoma. Described herein are novel somatic mutations in the ERBB4 gene that result in increased kinase activity, transformation ability and anchorage-independent growth. These ERBB4 mutations contribute to the tumorogenicity of melanoma. Thus, provided herein is a method of predicting the prognosis of a patient with melanoma by detecting the presence or absence of a mutation in the ERBB4 gene. In some examples, the ERBB4 mutation is selected from G949A, G1354A, G1624A, C1630T, G1687A, G2506A and G2614A (numbering based on SEQ ID NO: 1). Also provided are methods of selecting a patient as a candidate for treatment with an ERBB4 and/or PI3K/AKT pathway inhibitor, and a method of identifying a therapeutic agent for the treatment of a subject diagnosed with melanoma.

Abstract: Gene panels, microarrays and biomarker panels relating to genes and gene products associated with age-related oxidative damage to skin, and transcriptional profiling-based methods for identification and evaluation of cosmetic agents for prevention, reversal, or reduction of oxidative damage to skin. Cosmetic agents and compositions comprising the cosmetic agents, capable of inducing nrf2-mediated activation of the antioxidant response element to increase expression of Phase 2 enzymes, methods for restoring optimal redox status to skin employing the agents, and methods for identifying and evaluating cosmetic agents acting via the nrf2-mediated mechanism.

Abstract: The invention provides methods for producing a replication competent chimeric human immunodeficiency virus (HIV) that optionally contains a heterologous reporter gene, and methods for generating these viruses. The invention's recombinant viruses are useful in the determination of, for example, antiretroviral drug susceptibility, HIV drug resistance, HIV phenotyping, HIV genotyping, HIV fitness, HIV tropism or coreceptor usage, HIV serum neutralization, and for HIV vaccine development, HIV vector development, and HIV virus production.

Abstract: A debulking catheter comprising a tissue debulking assembly for removing a continuous strand of material from a body lumen. Catheters of the present invention generally include a catheter body having proximal and distal portions and a tissue debulking assembly disposed at least partially within the distal portion. The tissue debulking assembly is radially movable to expose at least a portion of the assembly through a window on the catheter body. The catheter is advanced transluminally through the body lumen to contact material in the body lumen and remove a plane of continuous material that has a length that is typically longer than a length of the window on the catheter. The continuous material may be directed into a collection chamber. Thereafter, the material may be removed from the collection chamber and preserved or tested.